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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaatgatgttcttcatcattgttttatatcatgcaatgcaaatgctacctatgtaattttcttcttaaactttgtgcagTACGCCAGATAATCATCAGAAGACTCTTGATCAGATTACCTTGCCTG

Basic information

species Zea mays
transcript GRMZM2G074818_T01
intron # 2
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|78117306|gb|DV535693.1|DV535693
EST:     ACACTAAATCTTGACGCCTTGAACTTGGATGACGCAATTTCTCTGATGGA                         TACGCCAGATAATCATCAGAAGACTCTTGATCAGATTACCTTGCCTG
genomic: ACACTAAATCTTGACGCCTTGAACTTGGATGACGCAATTTCTCTGATGGAgtaagtaatg ... ctttgtgcagTACGCCAGATAATCATCAGAAGACTCTTGATCAGATTACCTTGCCTG
EST: gi|28873763|gb|CB329707.1|CB329707
EST:     ACACTAAATCTTGACGCCTTGAACTTGGATGACGCAATTTCTCTGATGGA                         TACGCCAGATAATCATCAGAAGACTCTTGATCAGATTACCTTGCCTG
genomic: ACACTAAATCTTGACGCCTTGAACTTGGATGACGCAATTTCTCTGATGGAgtaagtaatg ... ctttgtgcagTACGCCAGATAATCATCAGAAGACTCTTGATCAGATTACCTTGCCTG
EST: gi|101390853|gb|EB817362.1|EB817362
EST:     ACACTAAATCTTGACGCCTTGAACTTGGATGACGCAATTTCTCTGATGGA                         TACGCCAGATAATCATCAGAAGACTCTTGATCAGATTACCTTGCCTG
genomic: ACACTAAATCTTGACGCCTTGAACTTGGATGACGCAATTTCTCTGATGGAgtaagtaatg ... ctttgtgcagTACGCCAGATAATCATCAGAAGACTCTTGATCAGATTACCTTGCCTG
EST: gi|74232287|gb|DT640201.1|DT640201
EST:     ACACTAAATCTTGACGCCTTGAACTTGGATGACGCAATTTCTCTGATGGA                         TACGCCAGATAATCATCAGAAGACTCTTGATCAGATTACCTTGCCCTG
genomic: ACACTAAATCTTGACGCCTTGAACTTGGATGACGCAATTTCTCTGATGGAgtaagtaatg ... ctttgtgcagTACGCCAGATAATCATCAGAAGACTCTTGATCAGATTACCTTGCC-TG
EST: gi|101384546|gb|EB814318.1|EB814318
EST:     ACACTAAATCTTGACGCCTTGAACTTGGATGACGCAATTTCTCTGATGGA                         TACGCCAGATAATCATCAGAAGACTCTTGATCAGATTACCTTGCCTG
genomic: ACACTAAATCTTGACGCCTTGAACTTGGATGACGCAATTTCTCTGATGGAgtaagtaatg ... ctttgtgcagTACGCCAGATAATCATCAGAAGACTCTTGATCAGATTACCTTGCCTG
EST: gi|71444958|gb|DR826008.1|DR826008
EST:     ACACTAAATCTTGACGCCTTGAACTTGGATGACGCAATTTCTCTGATGGA                         TACGCCAGATAATCATCAGAAGACTCTTGATCAGATTACCTTGCCTG
genomic: ACACTAAATCTTGACGCCTTGAACTTGGATGACGCAATTTCTCTGATGGAgtaagtaatg ... ctttgtgcagTACGCCAGATAATCATCAGAAGACTCTTGATCAGATTACCTTGCCTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 84

TTCCAATTGATGCAGACTGTGCTCCATTTGAGTCCATTACACTACCATCAACACTAAATCTTGACGCCTTGAACTTGGATGACGCAATTTCTCTGATGGAgtaagtaatg ... ctttgtgcagTACGCCAGATAATCATCAGAAGACTCTTGATCAGATTACCTTGCCTG


Block sizes: 44 (upstream exon), 42 (downstream exon)
Score: 13

TTCCAATTGATGCAGACTGTGCTCCATTTGAGTCCATTACACTACCATCAACACTAAATCTTGACGCCTTGAACTTGGATGACGCAATTTCTCTGATGGAgtaagtaatg ... ctttgtgcagTACGCCAGATAATCATCAGAAGACTCTTGATCAGATTACCTTGCCTG


Block sizes: 49 (upstream exon), 19 (downstream exon)
Score: 6

TTCCAATTGATGCAGACTGTGCTCCATTTGAGTCCATTACACTACCATCAACACTAAATCTTGACGCCTTGAACTTGGATGACGCAATTTCTCTGATGGAgtaagtaatg ... ctttgtgcagTACGCCAGATAATCATCAGAAGACTCTTGATCAGATTACCTTGCCTG


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 8

TTCCAATTGATGCAGACTGTGCTCCATTTGAGTCCATTACACTACCATCAACACTAAATCTTGACGCCTTGAACTTGGATGACGCAATTTCTCTGATGGAgtaagtaatg ... ctttgtgcagTACGCCAGATAATCATCAGAAGACTCTTGATCAGATTACCTTGCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatcatgcaatgcaaatgctacctatgtaattttcttcttaaactttgtgcagTACGCCAGATAATCATCAGAAGACTCTTGATCAGATTACCTTGCCTG
                             taattttcttcttaaa  TA-rich tract